I spy John Sheppard
by XX-Samantha-XX
Summary: Things seem to be happening to Sheppard and no one knows why, will they find out before it's too late.
1. The Plan: Phase one

Title: I Spy John Sheppard

Disclaimer: The characters aren't mine

Characters: Sheppard, McKay, Ronon, Teyla and the others

Summary: Things seem to be happening to Sheppard, no one knows why, will they find out in time or will they be too late?.

No spoilers

Have fun…

Chapter 1- The Plan: Phase one.

As soon as Darren set his eyes on John Sheppard again, he knew what he must do. He kept his distance for now. All he would do at the moment was observe Sheppard, see he how he worked, and see how to break him. During his observation of Sheppard he saw that, everyone on this place called Atlantis respected him. This respect he would destroy. He also saw that he ran every morning without fail. It had been a few days now since he had hidden in Atlantis, even all of his own people had now left. He had asked them, what the best way to break someone like Sheppard was. They had not agreed with the reason why he wanted to hurt Sheppard because, the people of Atlantis had rescued the entire village from certain doom. However, there was one they hadn't saved, Darren's brother; it had been Sheppard's fault. Or so Darren believed. When Darren had first met Sheppard he was grateful to meet him, he was rescuing them afterall. However, now he hated him and wanted to see the guy suffer. So he watched and waited, waited for the perfect time to strike.

Darren had been amazed at the vastness of Atlantis; it truly was a beautiful city, the ancestral city. He had heard about it from the myths of his home world. Sheppard didn't deserve to live in the great city. At fist he would make it look like Sheppard was just having accidents and then, he would step up his game plan, and use some of the techniques and medicines he had been told about to hurt Sheppard. He couldn't have people getting suspicious too early on. Ultimately, he wanted Sheppard dead but, that wasn't until much later on.

Darren spotted his target up ahead, Sheppard had ventured further than his usual route this morning. Darren liked that, it meant that Sheppard's friends wouldn't get to him as quick, leaving him time to escape. He figured to go for an embarrassing incident first, a simple trip-over. Darren laughed at the simple ness of it. Sheppard won't admit to falling down, far too embarrassing for the military commander to just fall down. Darren was hiding in a darkened corner. As his target approached he stuck his foot out. Sheppard's momentum carried him forward and straight into the wall as he tripped. Darren made sure that Sheppard wasn't moving when he escaped, fleeing to a room that was shielded from the sensors.

xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

TBC

Sorry it is so short the next chapter is longer, I just need to know if I should carry it on or not.

The next chapter will be up in a couple of days.


	2. AwakeningWatching, waiting and scheming

_Firstly, I'd just like to say thanks to all that left a review for the last chapter and, to those that had a few suggestions for later chapters. I will have fun with adding them in._

_For this chapter you see Beckett which is because I love his character and, I'm not sure how to do Keller. Though it is set around season 5 there are no spoilers as of yet but there will be in later chapters. Here we go then…_

Chapter 2- Awakening/Watching, waiting and scheming

"Sheppard?" asked a voice that Sheppard recognised, it was slightly panicked so could only be one person, Dr Rodney McKay. Sheppard was having a difficult time trying to remember what he had been doing, and why McKay was there. He vaguely remembered a mission going really wrong in fact, he had totally screwed up. Was that it, did he get hurt _again_? Was he in the infirmary _again_? Damn it, why can't he remember much he thought. Then, as he struggled back to consciousness he remembered a wall rushing towards him and now, he was on a hard cold floor, definitely not the infirmary.

"Sheppard? Damn it Sheppard, wake up!" the familiar voice half shouted, sounding more panicked than a moment ago, had it been a moment, Sheppard wasn't sure anymore. He decided that if he was going to get any answers, he would have to give into the voice and actually wake up.

McKay was becoming really worried for his friend especially, after finding him in an unconscious heap by the wall. McKay knew that Sheppard ran early in the morning but, it was now breakfast to which Sheppard always came to on time. Sheppard had been late so he went to search of him and, this is what he found. As he had walked towards Sheppard, he had the feeling that he was being watched, but shrugged it off as; the LSD in his hand hadn't found any life signs that were out of place.

x-X-x

What McKay didn't know, was that Darren was lurking somewhere close. Darren had asked around the other of his village, to see if there was anything that might hide him from the advanced sensors of the ancestral city. All but one of them knew nothing that would be able to help, or maybe they didn't want to help him carry out his plan. The last he spoke too seemed shady, Darren couldn't remember seeing this person before in his village but didn't question it, because this person knew of a device that could hide him. So, that is what he had done, hidden away while still watching what this person called McKay was doing with his target. He was still sure that his plan could be carried forward without being seen as; the device now around his wrist had hidden him from the sensor in McKay's hand.

Now Darren could begin to plan the next part of his plan, this part was to learn what Sheppard feared so it could be used to break him. Darren knew what sort of man Sheppard was, a man who would say that he was going to help and when they couldn't then they blamed them selves. Maybe, this was the way to do it, break Sheppard by playing on his failures. Darren had a sudden change of thought, he would not kill Sheppard, but leave him broken and not by physical means, though that would be fun as well. He snuck back to his 'room'; he started to get together some medicines and herbs. He had been taught how to make a certain drug by his new friend. His new friend seemed only eager to help…

x-X-x

Sheppard slowly opened his eyes to slits, and immediately shut them again as the light sent spikes of pain through his head; he had the mother of all headaches. He couldn't help moaning out in pain.

"Sheppard! Thank god, you're awake, why didn't you answer your radio? What happened? Why are you here anyway?" came the succession of questions from McKay. Sheppard moved to get up but thought better of it, nausea drove him back down, the pounding in his head increased as the questions came. He couldn't remember anything except that damn wall.

"Woah, stay still, I think you have a concussion, I'm calling Beckett" McKay said loudly enough to further increase Sheppard's ever growing headache.

"No… I'm fine… I just need to get my bearings" John was surprised to hear the slight weakness appear in his voice. He waited for the room to stop spinning as he opened his eyes once more, getting McKay into a blurred focus. Crap he thought. He suddenly had the feeling that he needed to expel his dinner from last night. He turned away from McKay, expelling anything his stomach held.

"Sheppard! That is just gross. Stay still, I'll call for help" Sheppard could just about hear a hushed one-sided conversation a few feet away. McKay had called Beckett and a med team. Sheppard wanted to at least make it to the infirmary under his own power. This want, was crushed as he felt the overwhelming need to sleep, as he fell into the darkness he could hear McKay shouting at him to stay awake. He just couldn't no matter how hard he tried. The voice faded and darkness welcomed him.

McKay was in full panic mode now, Sheppard had just this minute woke up and then fallen back unconscious again. This was so not good McKay thought. He knew that people with a concussion shouldn't fall asleep as, they may never wake up again. Just as he thought the worse, the doctor came rushing in.

"I thought I told ya to keep the lad awake" Carson sternly looked at McKay.

"I tried, oh god this is bad isn't it, is he going to die?" questions Rodney, he couldn't bare the thought.

He watched as the doctor tried and failed to wake Sheppard. He even thought he heard a muttered curse from the doctor, this really wasn't good. Carson and his team transferred the too still from of Sheppard to the gurney and rolled him away. McKay stood there in shocked silence for a moment; they were in Atlantis, how could things like this happen. Sheppard didn't just run into walls. There was something going on he thought. Then he thought that Sheppard was clumsy, and he hadn't seen anything on his scanner out of the ordinary. Maybe Sheppard would be able to tell him, when Sheppard woke up…

x-X-x

TBC

Sorry I know that it wasn't much longer than the first but here it is anyway. Still have plenty of accidents to plan (evil laugh)…more Shep to whump too…

The next chapters will be longer though you may have to wait longer sorry, I'm being distracted by my cross-over fic.


	3. Planting the seedsawakening, again

_Firstly those who have read he previous chapter will notice I've changed the summary, but it's still the same story. I just felt the new summary was better. _

_Thanks for all the reviews, favourites and alerts for the story so far, it's good to know that people actually like my writing. I was really worried about posting what I had written because of all the really good stories already on the site._

_Any medical stuff is researched but that doesn't make it right seen as I have no medical expertise what so ever._

Chapter 3- Planting the seeds/awakening, _again_.

With phase one complete, Darren could now get started on phase two. This part needed Sheppard out of his quarters for a short amount of time. The reason being, he needed to plant certain items within the room, secretly placed of course. One of the items that were going to be placed, had been given to him by his new 'friend', he had asked where it had been acquired but received only the answer that, is was from another world. He wasn't too bothered about where it had been obtained, as long as it did what it was suppose to. Darren had been told that the device was best used in conjunction with a certain drug. The drug, caused old nightmares to surface and, feel as real as being there again. Darren was looking forward to this part. Maybe, he would sneak in and watch the dreams play out. He didn't have to watch in person he would soon know Sheppard's worse nightmares and failures. The device, he had been told, could record a person's dreams whether good or bad. Darren had wondered why such a thing would be invented maybe, for the express purpose of torture or, so a person could deal with their dreams. Either way, Darren was going to use it for the purpose of breaking the man called Sheppard. Darren had also, been told that the drug if used too much could cause some negative side effects and, been told to use low doses. Though, he hadn't actually taken notice of the doses to be used, he just figured that he'd use what he saw fit. He had the feeling that this was the way to break Sheppard because, if he hadn't of been able to save his brother then, he probably hadn't been able to save others. Darren would use these two items along with others that he had come across. The purpose, to harm Sheppard, whether it be via use of weapons or poisons.

Perhaps, the way to break Sheppard's resolve was to keep him hurt. They may feel trapped by always getting hurt or get paranoid about someone being out to get them. While Sheppard wasn't a normal person, he could tell that he isn't the type not to want to be in control of what happens, he would feel that he had no control over what happened to him and hopefully, Darren thought that this would cause a crack in Sheppard's so called strength. Darren would make him think that he didn't belong here in Atlantis. Darren would practically drive Sheppard away from his friends; make him believe that he only caused them trouble. Isolate him. Make him believe that he himself had hurt his friends. Darren knew it would take a lot of work to break Sheppard away from his team but, at the end of it all, it would be worth it. Then, came the final phase, if the other phases had been successful then this final phase would be easier and the most satisfying so far, he would finally have his revenge, for his brother.

During Darren's observations, he notice that Sheppard hardly ever locked his quarters most likely because he felt safe, not for long Darren thought maliciously. Its seems that today was no different, he made it to his targets quarters with out being seen, he had left it to a time where there were less marines around and snuck past them. It was quite odd that he had yet to be caught as, all his people had been sent home maybe, if he had been seen, then others may have thought he was just a visiting Athosian. Theses people thought they were safe here, what little they know Darren thought. He would prove to them that they weren't even safe at home. When he was in the room he placed his items out if sight. The room itself was gloomy as he moved around. A few items that Darren didn't recognise were present; they obviously meant something to Sheppard, not that Darren cared. The sun was setting on the planet which created an eerie glow around the city. The last rays of light reflected off the interior walls and, gave off the atmosphere of, the warmness of a home at the same time of the day. Everyone here really was family to each other. Darren would enjoy destroying this family…

x-X-x

The first thing Sheppard heard on his way back to consciousness was, a soft accented voice, and it sounded very concerned. It was ordering him to wake up. He couldn't remember what had happened but, this time he knew he was in the infirmary. The voice grew louder as he became more aware. He had a killer headache, fuzzy images made their way around his mind again, all he could remember was that damned wall rushing at him.

"Come on lad, ya need to wake up" the voice was more forceful this time. "ya need to open ya eyes for me, than ya can go back ta sleep" the voice ordered.

Seen as Sheppard didn't think the voice was going to leave him alone otherwise then, he decided to comply with it. He opened his eyes to slits and, was met with a bright light. He winced at the brightness as it spiked his headache. He shut them to keep the light away and felt to tug of sleep. He shifted a little to try and wake him self up, he needed to know what happened. He felt the pinch of an IV drip in his right hand. How long had he been here he thought grimly.

"What happened?" he asked weakly. Both McKay and Beckett looked anxious as he voice this question. They looked like they hoped that he could answer that question. However, he couldn't no matter how hard he tried to think.

"Carson! You said would be fine, he can't even remember what happened. You and your voodoo…" McKay snapped but was cut off by Carson.

"Rodney! Ya know very well that a concussion can cause some memory loss, now be quite and stop disturbing my patients" Carson had gotten irritated to the point of thinking about using sedatives on the scientist but, restrained himself because he knew what McKay was like when he was scared. This fear had only increased in the hours that the Col had been brought into the infirmary, when he wouldn't respond to any outside stimuli. While Carson knew some memory loss was common, the concussion hadn't been that bad, and the fact that the Col had been unresponsive alarmed him. Not that Sheppard ever told him what was going on anyway; the lad was probably exhausted he thought. All the vitals were within normal range now, so hopefully nothing else was going on. He turned back to a sleepy looking Sheppard.

"What's the last thing ya remember lad?" Sheppard thought about the question, looking into his foggy memory and again remembered a metallic wall of Atlantis, he vaguely remembered running as well but nothing in between.

"erm…running…then a wall" he was unsure on the answer himself but, stuck to it in the hope maybe they could tell him. Beckett could see that the scientist was getting irritated with the answers from his friend and jumped in, before McKay could get started again.

"Ya gave us a bit of a scare lad, you were unresponsive when I got to ya and Rodney was in a panic" Carson heard a huff from the scientist. Sheppard frown a little, he didn't remember McKay being there at any point. Now he was worried about his memory loss, he hated loosing time, he'd done it enough times already. He hadn't meant to scare them. He hated when people worried about him. He would much rather do the protecting himself. Even as sleep pulled at him, he was about ready the get out of the infirmary so he could go back to his quarters and rest there, he hated staying in the infirmary. There was always too many people peeking in, wondering why you were there.

"Before ya ask, no, ya can't go back to yer quarters yet. Ya know the rules, now get some rest. I will come to check on ya in a little while" Sheppard gave Carson an innocent look, as if to say he wasn't thinking that exact thing. Carson shooed McKay away letting Sheppard rest quietly.

Dr Beckett heard the hushed voices and, was all ready to shoo McKay back out of the infirmary, this had become a common thing especially, if it were any of the team 'trapped' in the infirmary. However, he wasn't surprised to find that it was the other members of the Cols team. Ronon and Teyla moved quietly, unlike some, across the floor and headed his way. Carson figured that Rodney would have told them about what had happened to Sheppard, they looked a little worried. Teyla was the first to speak while; Ronon just hovered looking around for their team leader.

"We were told that Col Sheppard was here, is he alright?"

"Aye lass, he will be" Both Teyla and Ronon relaxed a little with this statement from the doctor.

"What happened?" asked Ronon in a tone both a little scary and caring at the same time, only Ronon and Teyla could do that. Ronon had become attached to his team over the 4 years here, this was home now, he knew they would look out for him and, he would do the same for them. It had been Col Sheppard who had brought him here and, for that he would always be grateful.

"We're not sure to be honest, he can't seem to remember anything, other than running this morning then waking up here" they all thought this a little concerning because anything could have happened to him. Though, they were on Atlantis, in relative safety, it was most likely an accident.

"May we see him?" smiled Teyla, she knew how Col Sheppard could find trouble, even in Atlantis.

"Aye ya can only for a moment though, we just got him settled."

Ronon and Teyla walked lightly towards Sheppard's usual bed when he was in the infirmary, so they wouldn't wake him. They looked upon him; he seemed just to be sleeping, no obvious signs of injury. The closer they studied his face; they could see a vivid bruise forming on his forehead though, his unruly hair did a good job of hiding it. They stood watching vigil over their friend for, the moment the doctor had allowed. Once they were sure he was resting peacefully, they headed for the mess hall where Rodney could be found, it was time for dinner after all…

x-X-x

A day or so later…

Sheppard had finally been released from the infirmary, after getting a talking to of course. He had only been allowed on light duty for then next couple of days, doctor's orders. He hated concussions; they had a way lingering over you, like a band playing in your head. Nothing a couple of Tylenol wouldn't cure he thought.

Sheppard strolled towards his room, basking in the glow and warmth that the sun had created within Atlantis. Over the past five years in the city, he had gotten used to the gentle hum of the city in the back of his mind. The hum always had a way of truly making him feel safe however; today the hum seemed a little off, something wasn't right. He had a feeling that he was being watched going back to his quarters. An uneasy feeling settled upon him. Maybe, McKay would know if anything was wrong with the city. There was no harm in asking, so he headed for the lab.

Couple of hours later…

Sheppard had spent a few hours trying to see if there was anything wrong, of course without McKay know why he was there; he had been made a Guinnipig for some devices the scientist had found. By the end of it all, the uneasy feeling had disappeared and Sheppard was feeling safe again. McKay hadn't been panicking so there was nothing major wrong with the city.

Sheppard headed back to his quarters so he could sleep. He became uneasy again heading to his quarters, as if the city was warning him against going there. However, he was so tired after spending most of the day with McKay, he didn't really notice. He also, didn't really feel the sting of a dart in his leg as walked lazily through his doors. One minute he was heading to his bed the next, he collapsed to the cold ground and slide into a fitful drugged sleep…

x-X-x

_TBC- I know I'm cruel with the cliff-hangers but it is fun (evil smile)_

_I'm not sure if this chapter came out right though, was being difficult so I'd like to know what you all think. Thanks for reading. _


	4. Stepping it upThe nightmares begin

_I thought that because I made you all wait so long for chapter 3 then I would do chapter 4 to. Thanks for the reviews everyone. So here goes chapter four, there will definitely be spoilers in this one. Again any medical stuff has been researched and may not be right. The bits in italics are from episodes or are dreams. _

Chapter 4-Stepping it up/The nightmares begin

When Darren had heard that Sheppard was being released from the infirmary, he planned the next part of his plan, this called for things to be stepped up. He had to talk to Sheppard, make him understand his situation. Make him push his friends away, make him not want to be here. He knew how to do this, if Sheppard didn't want to cooperate then, he would threaten Sheppard's friends. Get Sheppard under his control, he knew this would hurt Sheppard. Sheppard liked to be in control. Weeks of not being in control would break Sheppard, making him weak. Making him willing to do anything Darren said.

Darren waited for Sheppard to come to his quarters, he was getting excited at the prospect of finally getting to meet and hurt the man that had killed his brother. As soon as Sheppard entered the door of his quarters, Darren shot the dart at Sheppard's leg, he watched with a morbid fascination as Sheppard crumpled to the ground. The dart only held a small about of the drug in, enough to make Sheppard sleep for about half an hour. Darren hauled Sheppard limp figure up on to the bed and started tying Sheppard to the bed. He watched Sheppard in the throws of what looked like an emotional dream. At least that is what the device told him, the device its self was small and round in shape with a screen in the middle. The screen showed him the dream that was playing out in Sheppard's mind…

x-X-x

"_You may still think that you're Elizabeth, but you're not." Sheppard remembered saying. He also remembered the hurt look she gave him as he said it. This had been the last thing he had said to her when they were alone. As she walked through the gate, willingly to her death he remembered these words. When she had told the others that it was safe, he realised that he had been wrong, McKay had said _

"_I guess that answers the question as to whether it was really Elizabeth." As the others walked away, he just stood, shocked and numb. It took everything he had in him not to scream at that moment._

x-X-x

Darren would use the dream later on in the plan, for now he would just warn Sheppard. He noticed that the small screen went dark. Sheppard was waking up. Darren saw the shaking in Sheppard's body, and knew that his plan was already having the desired effects. He watched Sheppard regain consciousness. Now the fun can begin he thought excitedly…

x-X-x

Sheppard suddenly woke up shaking, the remembrance almost crushing him. He hadn't dreamed about that in months.

He became aware that someone was in his room. The figure had been watching him sleep. That's creepy thought Sheppard. Sheppard moved to get to the figure glaring at him, and was stopped by the fact he couldn't. His hands had been tied to the sides of his bed and, his feet to the foot of his bed. He was a little shocked by this as, he was usually a light sleeper and, the last thing he remembered he had fallen to the floor, not his bed. He struggled against the binds on his wrists, only to find that they dug in deeper. The figure loomed over him and spoke in a deep voice.

"You will suffer for what you have done."

"What?" Sheppard was confused as to who this person was, he didn't look familiar. He wasn't going to give the guy the satisfaction of looking scared though. He carried on his struggle to get free of the bonds. The guy smiled with a glint of evil in his eyes and punched Sheppard in the stomach. Sheppard grunted in pain, he wasn't going to scream, it just wasn't him. He took deep breaths until the pain subsided a little and spoke with defiance.

"What do you want?"

"For you to suffer" came the succinct reply from the shadows.

"Why?" Sheppard knew that he had angered lots of people, but he usually remembered who they were.

"All will become clear soon, there are just a few things I want for the moment and you _will_ allow it." Sheppard didn't like the sound of that.

"Like hell I will-" Sheppard was stopped by another punch to his stomach then carried on "you won't …get away with this" Sheppard said slightly strained.

"That! Is where you're wrong, you will do as I say. If you do not then I will kill your friends as they sleep." Darren let the statement settle upon his target. He could tell Sheppard was thinking carefully now. Ha gotcha Darren thought.

"There are guards all around this base; you'll never get to them." Sheppard half shouted, he struggling became more insistent.

"Then how have I not been seen yet and, how did I get to you?" Darren could see fear as the news sunk into Sheppard. Sheppard stopped struggling and lay there, not wanting to be the reason why his friends got hurt. This was not going to be fun he thought wryly.

Even in the dim light of his room, Sheppard saw Darren pull out a needle and head his way, he definitely didn't like where this was going. Darren could see a little fear in Sheppard's eyes; this made Darren smile even more. Sheppard spoke calmly.

"What is that?"

"Oh, this is where you nightmares begin Col Sheppard. I will soon learn all of your nightmares and, how to break you. You do not belong here!" Darren sneered. He could see that Sheppard still had his defiance, which would have to be fixed. He moved closer to Sheppard and plunged the needle into his arm. He knew the dose was too big but, also that the drug left the system in about six hours, so even if Sheppard went to the infirmary, he would not be believed.

Sheppard felt the pinch of the needle in his arm, and then the iciness of the liquid rushing through his body. His vision clouded and he became aware of falling. What he was falling into though, was anybody's guess. The clouds swirled around him and he was no longer in his room.

Darren watched as Sheppard lost consciousness and began the device he had hidden in the room. It already logged one small dream sequence. He hoped that what he was getting could be used against the man in front of him. The dreams would leave Sheppard tired and less resistant, as would the drug he had mixed with the one to cause the nightmares. Sheppard would be feeling very sick in the morning. He would leave a message for when Sheppard woke up, ordering him not to reveal what happened or what was wrong with him. He wrote the message and left it on Sheppard's side unit. He untied the binds and left the room. The device had come in a pair; one would be left with the victim and one he kept in his hidden room.

When Darren had gotten back to his new room, he took the other device and started watching the small dream sequence that had been recorded. When it was finished he sat back and smiled. He could use this one. The device beeped, signifying that a new dream sequence was in progress, the small screen showed what the Col was currently dreaming…

x-X-x

_Sheppard was all of a sudden running down the corridors of the Replicator version of Atlantis, along with Ronon. There they saw Elizabeth, holding Oberoth back with all she had. Sheppard called out to her, sounding very calm considering the circumstances.__"Elizabeth."_

_"Get to the Jumper." She stated, though her voice was strained._

_"You're coming with us." We don't leave our people behind Sheppard thought, and he was not going to leave Elizabeth behind, he couldn't. _

_Ronon fired his weapon at Oberoth. It had no effect. _

_"I can't keep them frozen much longer!" Elizabeth exclaims _

_"We're __not__ leaving you behind!" _

_"If you don't leave right now, __none__ of us will get out of here, so __go__." She pauses slightly and turns a little towards him, then continues "THAT'S AN ORDER!"_

_Oberoth notices the lapse in her concentration and the other Replicators start to move. One fires a weapon in Ronon's direction, he ducks and grabs Sheppard pulling him away. He shouts at Sheppard. _

"_Come on!"_

_As Sheppard is pulled away from her, he screamed in anguish "Elizabeth!"_

_The Replicators hurry down the corridor towards them, Elizabeth fully turns and yells "GO!"_

_Before they turn the corner Sheppard saw the frantic look in her face and then the Replicators grab her by the arms. He sees no more. He had just left her to them. He had just broken his primary rule, again. _

x-X-x

For the second time that night Sheppard woke up shaking, it seemed so real, like he had just relived that precise moment. The sounds, the smells and the emotions rushing him, making him feel drained. For a moment he couldn't remember where he was, he just lay there not wanting to move, he was numb, just like after that particular incident.

After a moment or two the emotions subsided a little and he remembered being tied up, he hoped that it had been a nightmare too. However, he hope was short live when a twinge in his abdomen reminded him he had been punched a couple of times. And then he remembered the warning and the needle. He, at that moment wished that it hadn't happened, and that the person that wanted him to suffer hadn't just witnessed one of his worse memories. He wanted to find the device and shut it off but he couldn't, he couldn't be the reason his friends got killed.

He looked over at the time 4am Atlantis time; there was no way he was going back to sleep tonight. He moved stiffly off his bed wincing slightly, as his muscles pulled. As he stood the room spun and little and he almost ended up back on his bed. That was when the nausea hit him; he stumbled to the bathroom, and barely made it to the toilet before he heaved until there was nothing in his stomach. When the retching had finished, he washed his face with shaking hands. He felt like crap and looked like it to, his hair was unusually messy and his skin pale. Hopefully no one noticed anything different. It was going to be hard though, he had to make sure no one got suspicious. His head was still a little foggy because of the drug he had been given. He was sore all over. His wrists were red and bleeding a little. He would have to hide that he thought grimly to himself. He hated the situation but could do nothing about it for the moment. He would figure something out…

x-X-x

Darren watched the two dreams for the second time; he couldn't believe that everyone respected this man called Sheppard. He had left the Atlantis's expedition leader in the hands of the enemy. For a man who said he never left anyone behind, Darren couldn't believe that he had left such an important person behind. While he wasn't aware of the whole situation he just guessed at the rest. He had what he needed for the moment. He would return to Sheppard in a couple of days for the next session. He would make Sheppard think that he wasn't going to do anything yet, then Darren was going to strike again when he least expected it. Darren would have fun with questioning Sheppard on his actions the next time they met…

TBC

_Not much of a cliff hanger but hopefully enough to make you want to keep reading. Hope you enjoyed it. Please read and review let me know what you think. _


	5. The nightmares continueEscape?

_I am really sorry this took so long to update, please don't kill me hehe, this chapter wasn't sounding right and I've had to rewrite it a few times and I was getting side tracked by one of my other fics, this chapter is also a little longer than the previous ones. Hope y'all like it and hope you're all still interested in the story. This chapter is a little more angsty than I thought it would be, but I believe its necessary after all that has happened over the years._

**Chapter 5- The nightmares continue/Escape?**

Darren had waited for another dream sequence to start, it never came. He wondered whether Sheppard was fighting sleep, not that it mattered, Sheppard would need to sleep sooner or later, when he did, Darren would enjoy watching the nightmares continue, he could wait. The next part of the plan would need the dreams to be twisted and used against his target. He would need to add a new ingredient to the drug to do this.

While he didn't have any plans for Sheppard for a couple of days, he still had to keep a careful eye on him and his friends. To make sure they didn't get suspicious. He had thought that leaving the note was pretty stupid, it could be found easily, he had to make sure that Sheppard wouldn't do anything to draw attention to the fact that he was being tortured. He also, assumed that Sheppard would know to keep it out of sight; Sheppard or one of his friends would pay for such an act of insubordination, and Sheppard knew it. If Darren was to hurt one of Sheppard's friends, he knew that Sheppard would blame himself which is what he wanted.

He couldn't exactly watch Sheppard, but he could listen to everything that was happening in Sheppard's room. He had managed to find what the Earthlings called 'bugging' equipment and had asked others how to use it; to everyone else, he seemed to be a visiting Athosian, just looking to protect the people he cared about. Nobody was any the wiser. Darren laughed at this, he thought that with the military running the security, they would have more security measures in place, not that it bothered him that they didn't.

x-X-x

Sheppard tiredly paced his room, muttering to himself about the amount of time he seemed to find trouble. It was like the galaxy was out to get him. He had barely stepped out of the infirmary and was in trouble _again, _the thing is, this time he couldn't ask for help, it was too dangerous for his friends. Maybe if his friends accidentally found out there wouldn't be any repercussions, would there? All this thinking was making Sheppard's head hurt though, that could have easily been the drugs effects. Whatever he had been given was forcing his stomach to rebel against him, his rushed to his bathroom to be sick for the third time since waking up. Each time exhausted him, but he couldn't do anything about it. After he had finished, he stood shakily and went back to his pacing, it seemed to be the only thing that calmed him at the moment.

He knew that if he went back to sleep, the nightmares would come back, he couldn't, they were too painful. He hadn't thought about them in a good couple of months. Thinking about the dreams, maybe, if he wasn't in his room the devices that had been planted couldn't force the dreams, not knowing that it was actually the drugs that caused them. He shuffled out of his room towards his pier, leaving the note out in the open, on his bedside table. He had seen it when he had woken, but had forgotten about it during his rambling and trying to find a way out of the situation. Leaving the note wasn't the best choice he had made, and someone would pay for it later.

When he stepped out intothe calming nature of pier, he fought the urge to be sick again as the cold salt air battered his weary body, stinging his grazed wrists a little as it blew. This is where he came to relax, to lose himself in the depths of the ocean, to think, the sounds of the waves lapping at Atlantis. When he couldn't fly and lose himself in the vastness of space, this is where he would be found. His friends would sometimes join him after a bad mission. His friends would also know when he needed to be alone. He wasn't sure whether he wanted them here or not, if he got them involved, he'd get them hurt. If he didn't they would be mad for him not trusting them to help him, like he would of helped them had they been in the same position. He could deal with the beatings and such, he was a solider after all, that is what he was trained for however, now that he had let people get close to him again, he couldn't, no wouldn't let them go or get them hurt, ultimately it would be the loneliness that would break him, that, and the fact Darren was dredging up his past failures, all at the same time. He had lived through them once, one at a time, not all together. He had just learned to live with himself again, after watching Elizabeth walk through the gate. The weight of them all would crush his optimism, break his spirit, he wouldn't be able to stop it, and he knew it.

He tried to shrug away his thoughts by looking at the golden horizon, the sun was peaking. He hadn't realized what time it was when he had grabbed the blankets from his quarters, and dragged him and them to the pier. Now he sat watching the sunrise, getting lost in its warmth. The warmth seeped into him, he dozed. The blankets had been the only thing he had taken from his room, the ocean while pretty, had a deceptively wintry breeze. Before he knew it he had fallen asleep, hopefully into a dreamless one, completely forgetting about a meeting that was due to start in a little under two hours…

x-X-x

Woolsey looked around at the faces of Atlantis's number one team, there was one missing and he was unusually late. The sense of unease grew as the person remained missing. A couple of minutes dragged into 10, they all looked around at each other sharing concerned glances well, all except McKay who was irritated by certain people being late.

"Would anyone like to tell me the whereabouts of Col. Sheppard?" asked Woolsey faking angry, while he didn't like tardiness; he knew something wasn't quite right, Ronon and Teyla showed as much in their posture. Teyla looked towards him worry evident in her brown eyes.

"We do not Mr. Woolsey, it is most unlike him." nodding in agreement he reached for his radio.

"Col. Sheppard, this is Woolsey, respond." after getting no answer it was Teyla's turn to try, speaking softly she asked.

"John? It is Teyla, are you there?" she couldn't keep the worry out of her voice and mind any longer. It really wasn't like him to not respond to radio calls, _and_ be late.

"Oh, come on, he's probably just sleeping." McKay piped up, then immediately shutting up when a warning glare from Teyla and Ronon found its way to him. "Fine, I'll go check his quarters" he moved towards the door, thinking this was stupid. Teyla turned to Woolsey, concern etched into her usually calm face.

"We will go and find him." she said with a sort of finality about it, as if she knew where he might be hiding. Though, he usually at least told one of them where he went, specifically so they didn't worry. She smiled serenely at the thought that John, might actually be hiding from these meetings, she knew he hated them.

x-X-x

Sheppard's quarters…

McKay strolled into Sheppard's quarters, not even stopping after opening the doors. He was frustrated that he had practically been forced intolooking for an absent Sheppard. Not that anyone would be able to find him via the sensors anyway, Atlantis had a habit of hiding him.

The first thing McKay noticed was, there was no blanket on the bed; the sheets looked a little ruffled. As he inspected the sheets closer, he saw blood specs. _Where'd they come from? _He thought fearfully. He hurried around the rest of the room seeing no signs of life, nothing out of place. However, he did see a note on the bed side table, he gasped as he read, then clicked on his radio.

"Ronon, Teyla, have you found him yet?" panic edging its way intohim.

"No, we have not. Is there something wrong?" she must have sensed the panic he thought; why else would she ask if there was anything wrong.

"Obviously there is something wrong, seen as he is missing. But other tha-" he was cut off by Ronon.

"McKay!" effectively ending the conversation, the radio went deadly silent.

His attention was drawn back to the note in his hands, the messy scrawl read;

'_Do not do anything that you will regret Sheppard, remember, I control you, and your friends. I will get my revenge. If you try to escape, I will know about it.'_

McKay didn't know what to do, should he tell someone? _Could_ he tell someone? Without getting Sheppard in trouble with who ever this guy was. What would this guy do? What had he already done? He scanned the room with his ever present tablet, not reading anything out of the ordinary. The last threat sent icy shivers down his spine. Who and how was he watching Sheppard and were they all really in danger. Out of his shocked silence the radio crackled to life.

"Rodney, we have found him." Came Teyla's voice over the radio, it sounded relieved yet there was something in it that worried him.

"Is…Is he okay?" McKay stuttered in reply, not sure he wanted the answer.

"He seems to be asleep, we are trying to wake him, but he is not responding to us. I believe that it would be best to call Dr Beckett."

"Yes, yes, ok, I will meet you in the infirmary as soon as I can; I just have to stop by my lab." He said thinking that he should try and find anything on the security cameras, or the Atlantis sensors which were more powerful, to see if he could find any evidence as to whom Sheppard is being threatened by.

"Very well" Teyla answered.

x-X-x

Elsewhere on Atlantis…

Darren heard movement in Sheppard's quarters, thinking it was Sheppard; he listened to what he was doing. He heard a voice mumbling, as it grew louder, he knew it was McKay's panicked ramblings. Darren's first thoughts were whether Sheppard had hid the note, and then from what he heard why were they trying to find Sheppard? Was he trying to escape?

He had to assume that McKay had found the note when, he heard his voice saying 'what the hell' then heard paper moving. One of the sensors was near the bed. Darren cursed Sheppard for leaving the note out, but then thought that could play right into his hands. Sheppard cared a lot about his friends, if any harm came to them by his own doing, it would break him quicker. Maybe this had worked out for the best after all….

x-X-x

Atlantis – The pier

At first, when Ronon and Teyla searched the pier they didn't find anything except the calming ocean, and the mid-morning sun hovering in the sky. They knew why Sheppard would come out here, it was calming and the rises or settings of the sun were beautiful.

As they turned back to the wonder of Atlantis, they saw a bundle of blankets. The blankets had a mess of familiar spiky hair peeking out of them, it had to be Sheppard. Ronon and Teyla, had seen this scene before, they smiled to one another thinking this same thought. They approached slowly so they would startle him.

"John?" Teyla called softly, kneeling down to move the blanket away from his face. As she took a closer look at John's face, she could see the weariness in it. Usually he looked peaceful while sleeping, unless he was having a nightmare.

"John?" Teyla called again, a little more forceful this time. She gently shook him, nothing, no response. This troubled her more than him not answering the radio; he was usually a light sleeper, even in the safety of Atlantis.

"Sheppard!" Ronon growled. When both their attempts failed, they shared a worried look. Their radios came to life with McKay's voice, asking them if they had found him yet, they didn't like the panic within it. They apprised him of the situation, turned to Sheppard, hoping that the conversation would rouse him.

Sheppard stirred, blinked slowly and lazily looked towards his friends. He couldn't hide the grimace that moving caused, or the hurt in his eyes. He had had the dreams again; he guessed _that_, that plan was out of the window. Now, to come up with one that worked, without his friends getting hurt. His friends' voices penetrated his thoughts. He slipped on his usual mask, and tried to reply as normal as possible.

"Hey guys-" he was going to say more, but the warning looks he received stopped him.

"John? We could not wake you, is there something wrong?" She knew that he wouldn't answer truthfully, but asked anyway. Maybe, the trust they had for each other would get an answer. He was very private, though they had learned a few things.

"I'm fine, just tired s'all, why are you here so early?" he answered a little wearily.

"You were late to the mission briefing, and would not answer your radio, so we came here."

"What…Wait…the briefing doesn't start yet." he stuttered confusedly, not knowing what to think. He had only closed his eyes for a few minutes, hadn't he?

"It started half an hour ago Sheppard." Ronon stated a little too forcefully, causing Sheppard to jump slightly. He would have laughed if it hadn't of been so out of character, was Sheppard scared of something? Teyla's eyes showed the same questions and fears as his.

Sheppard didn't know why Ronon had scared him a little; maybe, it was because he was looming over, just like Darren had during the night. Sheppard rose a little too quickly, he swayed and his vision faded a little. He would have landed back on the ground if he hadn't of been caught by his friends. When he managed to focus again, he knew that they wouldn't budge until he saw a doctor. He expected what came next.

"John, Dr Beckett is on his way." Sheppard gave Teyla a look to say don't bother, but she carried on. "We became worried, we thought it was best."

"Fine." Huffed Sheppard, not wanting his friends to worry too much about him, although, he did actually want their help, he just couldn't ask. He noticed that he was sat on the ground again, with his back against the wall. When did that happen? He must have zoned out, his mind was so fuzzy it was starting to worry even him. The next thing he knew Beckett was flashing that damned light in his eyes, he stopped the Doc before he started his lecture.

"Listen Doc, there's nothing wrong, I'm just tired, really" he wined, hoping to get out of going to the infirmary. He was scared of what the doctor would find in his system, it would mess the whole thing up, and then everyone would pay for it.

"The hell there's not lad, yer exhausted, when was the last time ya slept?" the accent sounded stronger, espically when the Doc was angry.

"Last night" Sheppard answered, trying to look honest, when he had been asleep the nightmares would come, whether in his room or not. This wasn't going to be fun, he hoped that Darren had some point to all this. "Doc, look, honestly, I just need some food and rest, then I'll be good as new"

"I'll be having none of that lad, I want ta keep an eye on ya for a while"

"But Doc-"

"No buts Col. unless of course ya can stand on ya own two feet, then you may go" Carson teased, knowing he'd try _and_ knowing he'd fail.

Trying to prove the Doctor wrong, Sheppard stood defiantly, swayed a little. He seemed to get his balance for a moment, then the nausea drove him back down, he collapsed and was sick. Sheppard was sure he didn't have anything left in him, except maybe the drug maybe that is what was causing this he thought. This last bout of sickness drained any energy he had; he slipped away into the darkness his dreams would bring.

Carson cursed as he watching what was happening, he now felt slightly guilty for letting Sheppard try. He hadn't expected that though, by the looks of the others' faces neither had they. All calm left Teyla as Sheppard collapsed, was sick, and then passed out. She caught his head before it hit the ground, into the mess he had just made.

"Dr Beckett, what is wrong with him?" she asked fearfully, while stroking back his messy hair from his warm forehead.

"I don't know lass, we need to get him to the infirmary" Carson answered honestly, while calling a team to bring a gurney. Beckett wondered briefly if he had missed something about Sheppard's recent head injury. However, the scans had come back clear. He had the feeling that something else was wrong…

TBC

Really sorry about the long wait, tell me what ya think of the new chapter and if you are still interested.


	6. Mistakes and Consequences

_Sorry for the long wait, I was trying to work out where to go seen as I have managed to change where I thought it was going. Really sorry about the wait, I was distracted by the NCIS fandom and my exams lol Hope you all like this next chapter._

**Chapter 6- Mistakes and Consequences**

McKay really wasn't sure whether or not he should just turn back now and tell someone like Ronon or Teyla. I mean, he wasn't exactly the type to do this sort of crazy stuff, he left that to Sheppard. He knew this thing- what ever it was, would need brains and brawn, no matter how much he wanted to be the best at fixing pretty much everything. Debating with himself, he barely noticed that he had reached his lab. Well. He was here now; he may as well check the sensors for any unusual readings or communications. He knew that Sheppard would do the same thing in his position, granted Sheppard would do it his own way, most likely getting something blown up in the process or having to use weapons. Sheppard was a military flyboy after all; one that seemed like a little kid at the prospect of battle, Ronon was the same.

Looking around at his usually food packed lab, he sighed as he only saw odd bits and bobs of ancient tech he had been trying to get Sheppard to activate. Sheppard needed help if the person was going to lengths to keep him quiet and threatening them, this guy was a danger to the security of the city. Moving with hates towards the stronger sensors for the city he got quickly absorbed in his work and didn't notice when Daren slipped silently into the room.

x-X-x

Now that Darren had dealt with McKay he needed to get back at Sheppard for being disobedient, he would have to wait until things settled down for the night but he would show what a mistake Sheppard had made. Looking at his own senor he tracked the amount of people around the infirmary area.

The dream device had been quite for a while now and he was getting bored, that is why he decided that McKay needed taking care of too, if he was found before he completed his plan then he wouldn't be able to get back a Sheppard. Sheppard deserved everything he was going to get. He was annoyed at the fact he wouldn't be able to drug Sheppard until later, he really wanted to see what other skeletons Sheppard was hiding.

As if sensing his boredom McKay started stirring, Darren smiled, now at least he could have a little fun.

x-X-x

Beckett shook his head a little while examining his most frequent patient. He wondered how Sheppard managed to find trouble, no matter where he was. he carried on with his examination; taking vitals and blood.

At first glance it just looked like exhaustion, which wasn't uncommon especially for Sheppard; he had a tendency for running himself into the ground. However, it was odd; it had been fairly quiet recently bar the odd few mishaps around base.

On second glance, however, upon completing the examination what he found disturbed him. There were abrasion on both wrists and ankles, as if being tied down to something, bruising on his stomach. Beckett didn't have a clue where they had come from, the team hadn't had a mission recently due to the refugees they had taken in and now taken somewhere safe. The usual after mission check-ups hadn't found anything like this, and all the people had been taken back over a week ago. Also, Sheppard hadn't been able to train with Ronon recently due to his head injury.

Beckett sighed heavily; he would have to ask Sheppard himself. Not that that would go over well with the Col. knowing Sheppard he would most likely have to go to Woolsey or at least someone who could get to the bottom of if without Sheppard having to know. Looking down at his patient he wished that Sheppard would just come to him whenever he was injured, knowing that wasn't going to happen, ever he moved away trying to think of others reasons for the injuries.

After pouring him self some much needed coffee he became concerned that Sheppard hadn't woken up yet, it had been several hours since he had collapsed and he wasn't responding to any attempts of getting him to wake up. Though, the dreams Sheppard must have been having were affecting him as it was effecting the readings as well, they were slightly erratic and a little worrying. He was just as surprised that McKay hadn't been to bug…see him yet, usually the rather exuberant scientist would have been already to down play medicine as any actual science and watch over Sheppard a little. Both Teyla and Ronon had already been a few times, each time he would assure them that Sheppard was just exhausted and would wake soon but that was a while ago and were getting concerned themselves.

Moving over to his desk with coffee and Sheppard file in his hand he passed a nurse who was carrying the blood test results. Settling him self down he rubbed his tired eyes a little and started making sense of results the test showed. Seeing nothing out of the ordinary he released a breath he didn't realise he had been hold, well at least is wasn't drugs he thought silently. But something didn't feel right he had been sure that something was going on, but just couldn't think of what.

Looking over the rest of the infirmary he noticed that Sheppard was his only patient at the moment, know there were a few nurses on shift he felt the drag of sleep upon him. Resting his head on his desk he fell asleep, it had been a long day after all…

x-X-x

_Finding him self walking around the deserted corridors of Atlantis, Sheppard tried to contact anyone, to see what the hell was going on. _

"_Sheppard to control room, respond?" he was getting a little scared, only a little though; there could be a perfectly valid reason that he seemed to be all alone. He hated being all alone though. _

"_Well that's where you're going to end up if you continue to kill your friends" a voice taunted, it sounded familiar though. He spun round to find himself standing face to face with Elizabeth. He was momentarily shocked and gasped. _

"_Why so shocked John." She sneered, the look in her eyes he hadn't seen before, not even when she had been telling him off for disobeying her. This one held a menace that he had only seen in tortures and wraith. _

_He tried to speak but found himself being thrown up against the wall, with her hand tightly grabbing his throat. What hell he tried to rasp but the words wouldn't form. He tried to push her away but failed the lack of oxygen making him weaker that he would like to admit. Where the hell had she got her strength from he wondered when she started talking again._

"_What? Did you think that you could leave me and never think about me again? I'm hurt I thought you didn't leave anyone behind, I thought that was you motto." She loosened her hold on him so he would rasp out his answer._

"_Y-you told me to follow the plan." _

"_No, John, you only heard what you wanted to hear so you could feel better about your self so your conscience wouldn't beat you're self up about it later. You let me walk into the trap."_

"_No…that's…not what happened…you told me to go. Ronon heard you too." He tried to plead but he believed what she said, maybe, he had only heard and remembered what he wanted so he would be able to live with it afterwards. I mean he felt guilty enough as it was over it so maybe she was right, maybe he had left her. The hand was tightened again, black started to enter his vision, the last thing he heard was;_

"_It's your fault I'm dead John, the others are going along with it so you won't get them killed. Even Rodney, who by the way isn't as safe as you think." With that the darkness took him._

x-X-x

Shooting up after the nightmare, the aches and pains of his body reasserted themselves. He was groggy and knew he needed to see a certain scientist was safe. He wouldn't be the cause of another friend's death. He was shaking a little as he turned the monitors off and took the IV out of the back of his hand. He needed to see Rodney, needed to escape this place for a little bit.

Sneaking out of the infirmary was easier than he expected, what he didn't notice was that Darren was watching him. Not until it was too late that is, he felt a sharp pain in his arm, he vision grew blurry and he fell to the ground with a thump. The last thing he saw before succumbing to the darkness for what felt like the third time today was a pair of unfamiliar feet…

TBC

_Well I know that it isn't that long but I had to get back into the swing of a Stargate Atlantis story again after all the NCIS I have been writing lately lol thanks for reading and please review even though I left you all waiting so long. _


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